In the statement the African Union Transition Mission in Somalia (ATMIS) said the helicopter, carrying eleven passengers including soldiers from Somalia military, was participating in training drills for casualty evacuation when the crash occurred.
"Regrettably, three of the eleven passengers on board lost their lives. Eight injured officers have been evacuated to Mogadishu for urgent medical attention," ATMIS said in the statement.
It did not give any details on casualties, including their nationality, but said investigations had begun to determine the cause of the crash.
ATMIS is assisting Somalia's central government in its war against the Islamist al Shabab insurgency.
The al Qaida-allied al Shabab group has been fighting for more than a decade to topple Somalia's government and establish its own rule based on its own strict interpretation of Islamic sharia law.